rs1009592

Positions:

• chr1-11868657-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.415 in 152,050 control chromosomes in the GnomAD database, including 14,375 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.41 (14375 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.967

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.415 AC: 63019 AN: 151932 Hom.: 14337 Cov.: 31

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.400

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.415 AC: 63100 AN: 152050 Hom.: 14375 Cov.: 31 AF XY: 0.408 AC XY: 30290 AN XY: 74326

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.277

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.399

Alfa AF: 0.381 Hom.: 1566

Bravo AF: 0.419

Asia WGS AF: 0.372 AC: 1292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.28
DANN	Benign	0.17

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1009592; hg19: chr1-11928714; COSMIC: COSV59923975;